Guang Mei,
Comparing these two depends partially on which version of NCBI Blast you
use. Until recently, NCBI emphasized speed over sensitivity. They caught
grief from it, so they changed things with the latest version (2.08). In my
tests, 2.08 takes about 100% longer to do a search compared to 2.05. I
haven't looked for any difference in sensitivity, although I have seen that
it fixes some other problems.
Marty
Martin Gollery
Bioinformatics
Timelogic Corp.
880 Northwood Blvd.
Suite 1
Incline Village, NV. 89451